jbrowse-plugin-msaview 5.14.0 → 5.14.1

package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -3,6 +3,7 @@ import { LoadingEllipses } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { MSAView } from 'react-msaview';
 import { makeStyles } from 'tss-react/mui';
+import { isLaunching } from '../isLaunching';
 import LaunchProgress from './LaunchProgress';
 const useStyles = makeStyles()({
     loadingContainer: {
@@ -11,20 +12,8 @@ const useStyles = makeStyles()({
 });
 const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
     const { classes } = useStyles();
-    const { blastParams, orthologParams, init, loadingStoredData } = model;
-    // an unresolved launch request means there is no alignment to draw yet, so all
-    // three gate the same panel -- see LaunchProgress. An indexed view keeps its
-    // init for the life of the view (it is how the block is refetched), so that
-    // one is only "launching" until the alignment arrives.
-    const request = blastParams ?? orthologParams;
-    const pending = !!request && !model.launchCompleted;
-    // a request that finished and then lost its alignment -- browser storage
-    // expires one after 7 days -- is a request again, and LaunchProgress draws it
-    // with the Retry that runs it. An error over an alignment still in hand is
-    // react-msaview's to draw.
-    const hasAlignment = !!(model.data.msa || model.data.tree);
-    const expired = !!request && !!model.error && !hasAlignment;
-    const launching = pending || expired || (!!init && !model.dataInitialized);
+    const { loadingStoredData } = model;
+    const launching = isLaunching(model);
     return (React.createElement("div", null, launching ? (React.createElement(LaunchProgress, { model: model })) : loadingStoredData && !model.dataInitialized ? (React.createElement("div", { className: classes.loadingContainer },
         React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model }))));
 });

package/dist/MsaViewPanel/isLaunching.d.ts

@@ -0,0 +1,22 @@
+interface LaunchState {
+    blastParams?: unknown;
+    orthologParams?: unknown;
+    launchCompleted?: boolean;
+    error?: unknown;
+    init?: unknown;
+    dataInitialized?: boolean;
+    data: {
+        msa?: string;
+        tree?: string;
+    };
+}
+/**
+ * Whether the panel draws LaunchProgress in place of the alignment. It does for
+ * a launch request still running, for a request whose alignment browser
+ * storage expired after 7 days (LaunchProgress offers a Retry), and for an init
+ * not yet fetched. An indexed view keeps its init for the life of the view, so
+ * it only launches until the alignment arrives. react-msaview draws an error
+ * over an alignment still in hand.
+ */
+export declare function isLaunching(model: LaunchState): boolean;
+export {};

package/dist/MsaViewPanel/isLaunching.js

@@ -0,0 +1,15 @@
+/**
+ * Whether the panel draws LaunchProgress in place of the alignment. It does for
+ * a launch request still running, for a request whose alignment browser
+ * storage expired after 7 days (LaunchProgress offers a Retry), and for an init
+ * not yet fetched. An indexed view keeps its init for the life of the view, so
+ * it only launches until the alignment arrives. react-msaview draws an error
+ * over an alignment still in hand.
+ */
+export function isLaunching(model) {
+    const request = model.blastParams ?? model.orthologParams;
+    const hasAlignment = !!(model.data.msa || model.data.tree);
+    return ((!!request && !model.launchCompleted) ||
+        (!!request && !!model.error && !hasAlignment) ||
+        (!!model.init && !model.dataInitialized));
+}

package/dist/MsaViewPanel/model.d.ts

@@ -1033,6 +1033,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * from. IndexedDB holds exactly these.
      */
     readonly unsavedDocuments: MsaDataPayload;
+    /**
+     * #getter
+     * true while a launch, stored data or a file is still loading and no
+     * error has ended it. jb.waitReady, the app's ready marker and
+     * screenshot tools read it for a view.
+     */
+    readonly showLoading: boolean;
 } & {
     /**
      * #action

package/dist/MsaViewPanel/model.js

@@ -6,6 +6,7 @@ import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, showDomainsOnGenomeIfAsked, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
 import { connectedDomains } from './connectedDomains';
 import { domainTrackConf } from './domainTrack';
+import { isLaunching } from './isLaunching';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
 import { syncSessionHighlights } from './sessionHighlights';
@@ -264,6 +265,18 @@ export default function stateModelFactory() {
                 gff: unsaved('gff', self.gffFilehandle),
             };
         },
+        /**
+         * #getter
+         * true while a launch, stored data or a file is still loading and no
+         * error has ended it. jb.waitReady, the app's ready marker and
+         * screenshot tools read it for a view.
+         */
+        get showLoading() {
+            return (!self.error &&
+                (isLaunching(self) ||
+                    (self.loadingStoredData && !self.dataInitialized) ||
+                    self.isLoading));
+        },
     }))
         .actions(self => ({
         /**

package/dist/MsaViewPanel/model.test.js

@@ -265,3 +265,28 @@ describe('connectedDomains', () => {
         });
     });
 });
+// jb.waitReady and the app's ready marker read showLoading, and read a view
+// without one as ready while its alignment is still being built
+describe('showLoading', () => {
+    test('a fresh view with nothing to load is not loading', () => {
+        expect(view().showLoading).toBe(false);
+    });
+    test('a running launch is loading until it fails', () => {
+        const model = view();
+        model.setBlastParams({ ...BLAST_PARAMS });
+        expect(model.showLoading).toBe(true);
+        model.setError(new Error('EBI said no'));
+        expect(model.showLoading).toBe(false);
+    });
+    test('a finished launch is not loading', async () => {
+        vi.mocked(doLaunchBlast).mockResolvedValue({
+            msa: '>a\nMK\n>b\nMK',
+            tree: '(a,b);',
+            treeMetadata: '{}',
+        });
+        const model = view();
+        model.setBlastParams({ ...BLAST_PARAMS });
+        await new Promise(res => setTimeout(res, 0));
+        expect(model.showLoading).toBe(false);
+    });
+});

package/dist/chunks/MsaViewPanel-MYCLHDTC.js

@@ -0,0 +1,2 @@
+import{a as P,b,d as k,e as J}from"./chunk-2MRW3C7A.js";import{d as M}from"./chunk-RTIGCYCA.js";import"./chunk-MDZDMDUF.js";import"./chunk-YTIKINP5.js";import"./chunk-IBVOKJV3.js";import"./chunk-YXL36I7H.js";import"./chunk-FCWXYIFC.js";import{a as B}from"./chunk-M2AAIXY5.js";import"./chunk-6GRHBYHB.js";import"./chunk-QWXSEUZI.js";import"./chunk-K55ZVN73.js";import{a as y}from"./chunk-NSASZ5FM.js";import"./chunk-EKTRLQV7.js";import"./chunk-W5VCM3IV.js";import"./chunk-4IRL4OLU.js";import"./chunk-73KAPCJ2.js";import"./chunk-Y7M36762.js";import{a as v}from"./chunk-CVLB4VFP.js";import{a as L}from"./chunk-DNFD5II2.js";import{a as w}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var a=i(p()),E=i(L()),T=i(v());var z=i(y());var o=i(p()),t=i(L()),n=i(w()),C=i(v()),V=i(y());var u=i(p()),S=i(w());function A({jobId:s}){let r=J(s)?k(s):b(s);return u.default.createElement(S.Typography,null,"Job ",s," (",u.default.createElement(B,{href:r},"see status"),")")}var d=A;var N=(0,V.makeStyles)()({margin:{padding:20},progressRow:{display:"flex",alignItems:"center",gap:12}}),U=(0,C.observer)(function({model:r}){let{progress:m,rid:e,error:l}=r,{classes:g}=N(),I=!r.launchCompleted,{blastParams:f,orthologParams:h}=r,c=f?`Running EBI ${f.searchProgram==="phmmer"?"phmmer":"BLAST"}`:h?h.source==="uniref"?"Building UniRef homolog alignment":"Building ortholog alignment":"Loading alignment";return o.default.createElement("div",{className:g.margin},l?o.default.createElement(o.default.Fragment,null,o.default.createElement(n.Typography,{variant:"h5"},I?`${c} failed`:"Alignment no longer available"),e?o.default.createElement(d,{jobId:e}):null,o.default.createElement(t.ErrorMessage,{error:l}),o.default.createElement("div",{className:g.progressRow},o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.retryLaunch()}},"Retry"),o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.cancelLaunch()}},"Dismiss"))):o.default.createElement(o.default.Fragment,null,o.default.createElement(t.LoadingEllipses,{message:c,variant:"h5"}),e?o.default.createElement(d,{jobId:e}):null,o.default.createElement("div",{className:g.progressRow},o.default.createElement(n.Typography,null,m||"Initializing"),o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.cancelLaunch()}},"Cancel"))))}),x=U;var D=(0,z.makeStyles)()({loadingContainer:{padding:20}}),$=(0,T.observer)(function({model:r}){let{classes:m}=D(),{loadingStoredData:e}=r,l=P(r);return a.default.createElement("div",null,l?a.default.createElement(x,{model:r}):e&&!r.dataInitialized?a.default.createElement("div",{className:m.loadingContainer},a.default.createElement(E.LoadingEllipses,{message:"Loading MSA data",variant:"h6"})):a.default.createElement(M,{model:r}))}),X=$;export{X as default};
+//# sourceMappingURL=MsaViewPanel-MYCLHDTC.js.map

package/dist/chunks/MsaViewPanel-MYCLHDTC.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/MsaViewPanel/components/MsaViewPanel.tsx", "../../src/MsaViewPanel/components/LaunchProgress.tsx", "../../src/MsaViewPanel/components/JobLink.tsx"],
+  "sourcesContent": ["import React from 'react'\n\nimport { LoadingEllipses } from '@jbrowse/core/ui'\nimport { observer } from 'mobx-react'\nimport { MSAView } from 'react-msaview'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { isLaunching } from '../isLaunching'\nimport LaunchProgress from './LaunchProgress'\n\nimport type { JBrowsePluginMsaViewModel } from '../model'\n\nconst useStyles = makeStyles()({\n  loadingContainer: {\n    padding: 20,\n  },\n})\n\nconst MsaViewPanel = observer(function MsaViewPanel2({\n  model,\n}: {\n  model: JBrowsePluginMsaViewModel\n}) {\n  const { classes } = useStyles()\n  const { loadingStoredData } = model\n  const launching = isLaunching(model)\n  return (\n    <div>\n      {launching ? (\n        <LaunchProgress model={model} />\n      ) : loadingStoredData && !model.dataInitialized ? (\n        <div className={classes.loadingContainer}>\n          <LoadingEllipses message=\"Loading MSA data\" variant=\"h6\" />\n        </div>\n      ) : (\n        <MSAView model={model} />\n      )}\n    </div>\n  )\n})\n\nexport default MsaViewPanel\n", "import React from 'react'\n\nimport { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport JobLink from './JobLink'\n\nimport type { JBrowsePluginMsaViewModel } from '../model'\n\nconst useStyles = makeStyles()({\n  margin: {\n    padding: 20,\n  },\n  progressRow: {\n    display: 'flex',\n    alignItems: 'center',\n    gap: 12,\n  },\n})\n\n/**\n * What a view shows while it is still building its alignment, and what it shows\n * when that fails.\n *\n * Every launch that resolves something states its request on the model --\n * `blastParams`, `orthologParams`, `init` -- and one not yet marked\n * `launchCompleted` IS \"no alignment yet\", as is a completed one whose stored\n * alignment has since expired. The error a failed launch records is only\n * readable here. This used to key on `blastParams` alone, which left an ortholog\n * launch rendering an empty MSAView for the minutes its alignment takes and, on\n * failure, forever: the error was set and nothing drew it.\n */\nconst LaunchProgress = observer(function LaunchProgress2({\n  model,\n}: {\n  model: JBrowsePluginMsaViewModel\n}) {\n  const { progress, rid, error } = model\n  const { classes } = useStyles()\n  // the request stays on the model after it succeeds, so an expired\n  // alignment's panel is still named after the search that built it\n  const pending = !model.launchCompleted\n  const { blastParams, orthologParams } = model\n  const message = blastParams\n    ? `Running EBI ${blastParams.searchProgram === 'phmmer' ? 'phmmer' : 'BLAST'}`\n    : orthologParams\n      ? orthologParams.source === 'uniref'\n        ? 'Building UniRef homolog alignment'\n        : 'Building ortholog alignment'\n      : 'Loading alignment'\n  return (\n    <div className={classes.margin}>\n      {error ? (\n        <>\n          <Typography variant=\"h5\">\n            {pending ? `${message} failed` : 'Alignment no longer available'}\n          </Typography>\n          {/* the job outlives the browser, so its link is worth keeping next to\n              the failure -- EBI's own page says more about a job than we can */}\n          {rid ? <JobLink jobId={rid} /> : null}\n          <ErrorMessage error={error} />\n          {/* the request stays on the model after a failure, so without these\n              the view is a dead end that resubmits the job on every reload */}\n          <div className={classes.progressRow}>\n            <Button\n              variant=\"outlined\"\n              size=\"small\"\n              onClick={() => {\n                model.retryLaunch()\n              }}\n            >\n              Retry\n            </Button>\n            <Button\n              variant=\"outlined\"\n              size=\"small\"\n              onClick={() => {\n                model.cancelLaunch()\n              }}\n            >\n              Dismiss\n            </Button>\n          </div>\n        </>\n      ) : (\n        <>\n          <LoadingEllipses message={message} variant=\"h5\" />\n          {rid ? <JobLink jobId={rid} /> : null}\n          <div className={classes.progressRow}>\n            <Typography>{progress || 'Initializing'}</Typography>\n            {/* stops the polling and returns to the import form; the EBI job\n                itself runs on regardless, which is what its JobLink is for */}\n            <Button\n              variant=\"outlined\"\n              size=\"small\"\n              onClick={() => {\n                model.cancelLaunch()\n              }}\n            >\n              Cancel\n            </Button>\n          </div>\n        </>\n      )}\n    </div>\n  )\n})\n\nexport default LaunchProgress\n", "import React from 'react'\n\nimport { Typography } from '@mui/material'\n\nimport ExternalLink from '../../components/ExternalLink'\nimport { ebiBlastResultUrl } from '../../utils/ebiBlast'\nimport { isPhmmerJobId, phmmerResultUrl } from '../../utils/phmmer'\n\nfunction JobLink({ jobId }: { jobId: string }) {\n  // read off the job id rather than the launch params, so a link rebuilt for an\n  // old cached job still points at the tool that actually ran it\n  const url = isPhmmerJobId(jobId)\n    ? phmmerResultUrl(jobId)\n    : ebiBlastResultUrl(jobId)\n  return (\n    <Typography>\n      Job {jobId} (<ExternalLink href={url}>see status</ExternalLink>)\n    </Typography>\n  )\n}\n\nexport default JobLink\n"],
+  "mappings": "ouBAAA,IAAAA,EAAkB,OAElBC,EAAgC,OAChCC,EAAyB,OAEzB,IAAAC,EAA2B,OCL3B,IAAAC,EAAkB,OAElBC,EAA8C,OAC9CC,EAAmC,OACnCC,EAAyB,OACzBC,EAA2B,OCL3B,IAAAC,EAAkB,OAElBC,EAA2B,OAM3B,SAASC,EAAQ,CAAE,MAAAC,CAAM,EAAsB,CAG7C,IAAMC,EAAMC,EAAcF,CAAK,EAC3BG,EAAgBH,CAAK,EACrBI,EAAkBJ,CAAK,EAC3B,OACE,EAAAK,QAAA,cAAC,kBAAW,OACLL,EAAM,KAAE,EAAAK,QAAA,cAACC,EAAA,CAAa,KAAML,GAAK,YAAU,EAAe,GACjE,CAEJ,CAEA,IAAOM,EAAQR,EDVf,IAAMS,KAAY,cAAW,EAAE,CAC7B,OAAQ,CACN,QAAS,EACX,EACA,YAAa,CACX,QAAS,OACT,WAAY,SACZ,IAAK,EACP,CACF,CAAC,EAcKC,KAAiB,YAAS,SAAyB,CACvD,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,SAAAC,EAAU,IAAAC,EAAK,MAAAC,CAAM,EAAIH,EAC3B,CAAE,QAAAI,CAAQ,EAAIN,EAAU,EAGxBO,EAAU,CAACL,EAAM,gBACjB,CAAE,YAAAM,EAAa,eAAAC,CAAe,EAAIP,EAClCQ,EAAUF,EACZ,eAAeA,EAAY,gBAAkB,SAAW,SAAW,OAAO,GAC1EC,EACEA,EAAe,SAAW,SACxB,oCACA,8BACF,oBACN,OACE,EAAAE,QAAA,cAAC,OAAI,UAAWL,EAAQ,QACrBD,EACC,EAAAM,QAAA,gBAAAA,QAAA,cACE,EAAAA,QAAA,cAAC,cAAW,QAAQ,MACjBJ,EAAU,GAAGG,CAAO,UAAY,+BACnC,EAGCN,EAAM,EAAAO,QAAA,cAACC,EAAA,CAAQ,MAAOR,EAAK,EAAK,KACjC,EAAAO,QAAA,cAAC,gBAAa,MAAON,EAAO,EAG5B,EAAAM,QAAA,cAAC,OAAI,UAAWL,EAAQ,aACtB,EAAAK,QAAA,cAAC,UACC,QAAQ,WACR,KAAK,QACL,QAAS,IAAM,CACbT,EAAM,YAAY,CACpB,GACD,OAED,EACA,EAAAS,QAAA,cAAC,UACC,QAAQ,WACR,KAAK,QACL,QAAS,IAAM,CACbT,EAAM,aAAa,CACrB,GACD,SAED,CACF,CACF,EAEA,EAAAS,QAAA,gBAAAA,QAAA,cACE,EAAAA,QAAA,cAAC,mBAAgB,QAASD,EAAS,QAAQ,KAAK,EAC/CN,EAAM,EAAAO,QAAA,cAACC,EAAA,CAAQ,MAAOR,EAAK,EAAK,KACjC,EAAAO,QAAA,cAAC,OAAI,UAAWL,EAAQ,aACtB,EAAAK,QAAA,cAAC,kBAAYR,GAAY,cAAe,EAGxC,EAAAQ,QAAA,cAAC,UACC,QAAQ,WACR,KAAK,QACL,QAAS,IAAM,CACbT,EAAM,aAAa,CACrB,GACD,QAED,CACF,CACF,CAEJ,CAEJ,CAAC,EAEMW,EAAQZ,EDlGf,IAAMa,KAAY,cAAW,EAAE,CAC7B,iBAAkB,CAChB,QAAS,EACX,CACF,CAAC,EAEKC,KAAe,YAAS,SAAuB,CACnD,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIH,EAAU,EACxB,CAAE,kBAAAI,CAAkB,EAAIF,EACxBG,EAAYC,EAAYJ,CAAK,EACnC,OACE,EAAAK,QAAA,cAAC,WACEF,EACC,EAAAE,QAAA,cAACC,EAAA,CAAe,MAAON,EAAO,EAC5BE,GAAqB,CAACF,EAAM,gBAC9B,EAAAK,QAAA,cAAC,OAAI,UAAWJ,EAAQ,kBACtB,EAAAI,QAAA,cAAC,mBAAgB,QAAQ,mBAAmB,QAAQ,KAAK,CAC3D,EAEA,EAAAA,QAAA,cAACE,EAAA,CAAQ,MAAOP,EAAO,CAE3B,CAEJ,CAAC,EAEMQ,EAAQT",
+  "names": ["import_react", "import_ui", "import_mobx_react", "import_mui", "import_react", "import_ui", "import_material", "import_mobx_react", "import_mui", "import_react", "import_material", "JobLink", "jobId", "url", "isPhmmerJobId", "phmmerResultUrl", "ebiBlastResultUrl", "React", "ExternalLink", "JobLink_default", "useStyles", "LaunchProgress", "model", "progress", "rid", "error", "classes", "pending", "blastParams", "orthologParams", "message", "React", "JobLink_default", "LaunchProgress_default", "useStyles", "MsaViewPanel", "model", "classes", "loadingStoredData", "launching", "isLaunching", "React", "LaunchProgress_default", "Loading_default", "MsaViewPanel_default"]
+}

package/dist/chunks/chunk-2MRW3C7A.js

@@ -0,0 +1,2 @@
+import{j as u,p as l,q as h,u as p}from"./chunk-6GRHBYHB.js";function q(t){let n=t.blastParams??t.orthologParams,e=!!(t.data.msa||t.data.tree);return!!n&&!t.launchCompleted||!!n&&!!t.error&&!e||!!t.init&&!t.dataInitialized}var g="ncbiblast";function f(t){return(t.hits??[]).map(n=>{let e=Number.parseInt(n.hit_uni_ox??"",10);return{accession:n.hit_acc??"unknown",id:n.hit_id??n.hit_acc??"unknown",sciname:n.hit_uni_os??n.hit_os??"unknown",taxid:Number.isNaN(e)?void 0:e,title:n.hit_uni_de??n.hit_desc,sequence:(n.hit_hsps?.[0]?.hsp_hseq??"").replaceAll("-","")}})}function A(t){return`https://www.ebi.ac.uk/jdispatcher/sss/${g}/summary?jobId=${t}`}async function w({query:t,blastDatabase:n,maxHits:e,onProgress:s,onRid:r,signal:i}){let a=String(h(e??l)),o=await u({tool:g,label:"BLAST",params:{program:"blastp",stype:"protein",database:n,sequence:t,alignments:a,scores:a},onProgress:s,onRid:r,signal:i});return{rid:o.jobId,hits:f(JSON.parse(await o.result("json")))}}var I=({database:t,...n})=>w({blastDatabase:t,...n});var m="hmmer3_phmmer";function H(t){return`https://www.ebi.ac.uk/jdispatcher/sss/${m}/summary?jobId=${t}`}function N(t){return t.startsWith(`${m}-`)}function x({rf:t,query:n}){let e=0,s=Array.from(t,r=>r==="x"?n[e++]??"-":"-").join("");if(e!==n.length)throw new Error(`phmmer alignment has ${e} match columns for a query of ${n.length} residues, so the query row cannot be placed`);return s}function _(t){let n=(t??"").replace("[subseq from] ","");if(n.includes("^|^")){let r=n.split("^|^"),i=r[6];return{id:r[0]||void 0,sciname:r[5]||"unknown",taxid:i&&/^\d+$/.test(i)?Number.parseInt(i,10):void 0,title:r[2]||void 0}}let e=/OS=(.*?)\s+(?:OX|GN|PE|SV)=/.exec(n)?.[1],s=/OX=(\d+)/.exec(n)?.[1];return{id:void 0,sciname:e??"unknown",taxid:s?Number.parseInt(s,10):void 0,title:n.split(" OS=")[0]||void 0}}function S(t){let n=t.lastIndexOf("/"),e=n===-1?void 0:/^\d+-\d+$/.exec(t.slice(n+1))?.[0],s=e===void 0?t:t.slice(0,n),r=s.split("|");return r.length===3?{accession:r[1],id:r[2],range:e}:{accession:s,id:s,range:e}}function y({stockholm:t,query:n}){let{gc:e,gs:s,seqdata:r,seqname:i}=new p(t,0).getMSA(),a=e.RF;if(!a)throw new Error("phmmer alignment has no #=GC RF line");return{queryRow:x({rf:a,query:n}),rows:i.map(o=>{let{id:d,...b}=_(s.DE?.[o]?.[0]),c=S(o);return{...c,id:c.id===c.accession&&d?d:c.id,...b,aligned:(r[o]??"").replaceAll(".","-").toUpperCase()}})}}async function P({query:t,database:n,maxHits:e,onProgress:s,onRid:r,signal:i}){let a=await u({tool:m,label:"phmmer",params:{database:n,sequence:t,alignView:"true",...e?{nhits:String(e)}:{}},onProgress:s,onRid:r,signal:i});return{rid:a.jobId,...y({stockholm:await a.result("sto"),query:t})}}function k(t){return t.map(({aligned:n,...e})=>({...e,sequence:n}))}var $=async({database:t,...n})=>{let{rows:e,queryRow:s,rid:r}=await P({database:t,...n});return{rid:r,queryRow:s,hits:k(e)}};export{q as a,A as b,I as c,H as d,N as e,$ as f};
+//# sourceMappingURL=chunk-2MRW3C7A.js.map

package/dist/chunks/chunk-2MRW3C7A.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/MsaViewPanel/isLaunching.ts", "../../src/utils/ebiBlast.ts", "../../src/utils/phmmer.ts"],
+  "sourcesContent": ["interface LaunchState {\n  blastParams?: unknown\n  orthologParams?: unknown\n  launchCompleted?: boolean\n  error?: unknown\n  init?: unknown\n  dataInitialized?: boolean\n  data: { msa?: string; tree?: string }\n}\n\n/**\n * Whether the panel draws LaunchProgress in place of the alignment. It does for\n * a launch request still running, for a request whose alignment browser\n * storage expired after 7 days (LaunchProgress offers a Retry), and for an init\n * not yet fetched. An indexed view keeps its init for the life of the view, so\n * it only launches until the alignment arrives. react-msaview draws an error\n * over an alignment still in hand.\n */\nexport function isLaunching(model: LaunchState) {\n  const request = model.blastParams ?? model.orthologParams\n  const hasAlignment = !!(model.data.msa || model.data.tree)\n  return (\n    (!!request && !model.launchCompleted) ||\n    (!!request && !!model.error && !hasAlignment) ||\n    (!!model.init && !model.dataInitialized)\n  )\n}\n", "import {\n  defaultMaxHits,\n  snapBlastHitCount,\n} from '../LaunchMsaView/components/BlastQuery/consts'\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { BlastDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend, SearchHit } from './homologSearch'\n\nconst TOOL = 'ncbiblast'\n\n/**\n * The subset of EBI's ncbiblast JSON result this plugin reads. The service\n * returns a great deal more per hit (urls, bit scores, e-values, the match\n * string); only what the MSA rows are built from is typed here.\n */\ninterface EbiBlastJson {\n  hits?: {\n    hit_acc?: string\n    hit_id?: string\n    hit_desc?: string\n    /** the UniProt fields are absent on hits from non-UniProt databases */\n    hit_os?: string\n    hit_uni_de?: string\n    hit_uni_os?: string\n    /** NCBI taxon id, delivered as a string */\n    hit_uni_ox?: string\n    hit_hsps?: { hsp_hseq?: string }[]\n  }[]\n}\n\n/**\n * EBI's hits as search hits. BLAST's alignments are pairwise, one hit at a\n * time, so the gaps come back off and an aligner gets bare sequences. Exported\n * for testing against a captured response: nothing else in CI would notice if\n * EBI renamed a field.\n */\nexport function normalizeEbiBlastHits(result: EbiBlastJson): SearchHit[] {\n  return (result.hits ?? []).map(hit => {\n    const taxid = Number.parseInt(hit.hit_uni_ox ?? '', 10)\n    return {\n      accession: hit.hit_acc ?? 'unknown',\n      id: hit.hit_id ?? hit.hit_acc ?? 'unknown',\n      sciname: hit.hit_uni_os ?? hit.hit_os ?? 'unknown',\n      taxid: Number.isNaN(taxid) ? undefined : taxid,\n      // hit_uni_de is the bare protein name; hit_desc repeats it with the\n      // OS=/OX=/GN= suffix that makeId already covers with real columns\n      title: hit.hit_uni_de ?? hit.hit_desc,\n      sequence: (hit.hit_hsps?.[0]?.hsp_hseq ?? '').replaceAll('-', ''),\n    }\n  })\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error \u2014 so it has to\n * be EBI's own results UI, not the REST result endpoint, which does not exist\n * yet at the moment the link is on screen.\n */\nexport function ebiBlastResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\nexport async function queryEbiBlast({\n  query,\n  blastDatabase,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  blastDatabase: BlastDatabase\n  /** rounded up to a count EBI accepts */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const hitCount = String(snapBlastHitCount(maxHits ?? defaultMaxHits))\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'BLAST',\n    params: {\n      program: 'blastp',\n      stype: 'protein',\n      database: blastDatabase,\n      sequence: query,\n      alignments: hitCount,\n      scores: hitCount,\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  return {\n    rid: job.jobId,\n    hits: normalizeEbiBlastHits(\n      JSON.parse(await job.result('json')) as EbiBlastJson,\n    ),\n  }\n}\n\nexport const searchEbiBlast: SearchBackend = ({ database, ...request }) =>\n  queryEbiBlast({ blastDatabase: database as BlastDatabase, ...request })\n", "import { StockholmMSA } from 'msa-parsers'\n\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend, SearchHit } from './homologSearch'\n\nconst TOOL = 'hmmer3_phmmer'\n\nexport interface PhmmerRow {\n  accession: string\n  id: string\n  sciname: string\n  taxid?: number\n  title?: string\n  /** the matched envelope on the target, e.g. '503-912', absent if unparseable */\n  range?: string\n  /** the row as phmmer aligned it, uppercased with '.' inserts turned into '-' */\n  aligned: string\n}\n\nexport interface PhmmerAlignment {\n  rows: PhmmerRow[]\n  /**\n   * the query, placed into the same columns. phmmer does not put the query in\n   * its own output, so this is derived \u2014 see buildQueryRow.\n   */\n  queryRow: string\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error.\n *\n * The category has to be sss: jdispatcher serves its shell with a 200 for any\n * category, so /pfa/ and /psa/ look fine to a fetch and render \"Page Not Found\"\n * in a browser.\n */\nexport function phmmerResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\n/** EBI job ids are prefixed with the tool that made them */\nexport function isPhmmerJobId(jobId: string) {\n  return jobId.startsWith(`${TOOL}-`)\n}\n\n/**\n * phmmer aligns every hit to a profile built from the query, one match state\n * per query residue, and marks those columns 'x' in #=GC RF. So the query's own\n * row is exactly recoverable: walk RF, consume a query residue at each match\n * column, gap everywhere else.\n *\n * This is the one piece of real logic here rather than a library call, and it\n * is checked hard: if the match columns do not account for the query exactly,\n * the columns and the query have drifted apart, and a query row that is off by\n * even one residue would silently mis-map every column to the genome. Throwing\n * is much better than drawing that.\n */\nfunction buildQueryRow({ rf, query }: { rf: string; query: string }) {\n  let consumed = 0\n  const row = Array.from(rf, c =>\n    c === 'x' ? (query[consumed++] ?? '-') : '-',\n  ).join('')\n  if (consumed !== query.length) {\n    throw new Error(\n      `phmmer alignment has ${consumed} match columns for a query of ${query.length} residues, so the query row cannot be placed`,\n    )\n  }\n  return row\n}\n\n/**\n * '[subseq from] Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2' is what a\n * UniProt target's #=GS DE looks like. The representative-proteome databases\n * (rp15..rp75) write the same facts as caret-pipe fields instead --\n * 'P53_HUMAN^|^DNHU53^|^Cellular tumor antigen p53^|^...^|^Homo sapiens^|^9606^|^Euk/mammal^|^40674'\n * -- so both grammars are read. Hits from the non-UniProt databases phmmer\n * also offers (PDB, AlphaFold, MEROPS...) carry neither, so every field here\n * is optional.\n */\nfunction parseDescription(de: string | undefined) {\n  const text = (de ?? '').replace('[subseq from] ', '')\n  if (text.includes('^|^')) {\n    const fields = text.split('^|^')\n    const ox = fields[6]\n    return {\n      id: fields[0] || undefined,\n      sciname: fields[5] || 'unknown',\n      taxid: ox && /^\\d+$/.test(ox) ? Number.parseInt(ox, 10) : undefined,\n      title: fields[2] || undefined,\n    }\n  }\n  const sciname = /OS=(.*?)\\s+(?:OX|GN|PE|SV)=/.exec(text)?.[1]\n  const ox = /OX=(\\d+)/.exec(text)?.[1]\n  return {\n    id: undefined,\n    sciname: sciname ?? 'unknown',\n    taxid: ox ? Number.parseInt(ox, 10) : undefined,\n    title: text.split(' OS=')[0] || undefined,\n  }\n}\n\n/**\n * Target names look like 'sp|P02768|ALBU_HUMAN/1-609' for UniProt databases and\n * like anything at all for the others, so an unrecognized name becomes its own\n * accession rather than being dropped.\n */\nfunction parseName(name: string) {\n  const slash = name.lastIndexOf('/')\n  const range =\n    slash === -1 ? undefined : /^\\d+-\\d+$/.exec(name.slice(slash + 1))?.[0]\n  const bare = range === undefined ? name : name.slice(0, slash)\n  const parts = bare.split('|')\n  return parts.length === 3\n    ? { accession: parts[1]!, id: parts[2]!, range }\n    : { accession: bare, id: bare, range }\n}\n\n/**\n * Exported for testing against a captured .sto \u2014 the annotation names (RF, the\n * DE line's OS=/OX=) are the whole risk in this mapping, and nothing else in CI\n * would notice if HMMER or EBI changed one.\n */\nexport function parsePhmmerAlignment({\n  stockholm,\n  query,\n}: {\n  stockholm: string\n  query: string\n}): PhmmerAlignment {\n  const { gc, gs, seqdata, seqname } = new StockholmMSA(stockholm, 0).getMSA()\n  const rf = gc.RF\n  if (!rf) {\n    throw new Error('phmmer alignment has no #=GC RF line')\n  }\n\n  return {\n    queryRow: buildQueryRow({ rf, query }),\n    rows: seqname.map(name => {\n      const { id, ...description } = parseDescription(gs.DE?.[name]?.[0])\n      const parsed = parseName(name)\n      return {\n        ...parsed,\n        // the rp databases name a row by bare accession and put the mnemonic\n        // id in the description instead\n        id: parsed.id === parsed.accession && id ? id : parsed.id,\n        ...description,\n        // insert columns come back lowercase with '.' for gaps; the MSA renderer\n        // looks colors up by the literal letter, so lowercase would draw\n        // uncolored. The insert columns stay visible as gaps in the query row.\n        aligned: (seqdata[name] ?? '').replaceAll('.', '-').toUpperCase(),\n      }\n    }),\n  }\n}\n\nexport async function queryPhmmer({\n  query,\n  database,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  database: PhmmerDatabase\n  /** EBI's `nhits`, 100 when omitted */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'phmmer',\n    params: {\n      database,\n      sequence: query,\n      // the alignment is the whole point of using phmmer here\n      alignView: 'true',\n      ...(maxHits ? { nhits: String(maxHits) } : {}),\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  return {\n    rid: job.jobId,\n    ...parsePhmmerAlignment({ stockholm: await job.result('sto'), query }),\n  }\n}\n\n/** phmmer's rows as search hits: the aligned row is the hit's sequence. */\nexport function toSearchHits(rows: PhmmerRow[]): SearchHit[] {\n  return rows.map(({ aligned, ...rest }) => ({ ...rest, sequence: aligned }))\n}\n\n/**\n * phmmer as a search backend. It aligns every hit to a profile of the query as\n * it searches, so the result carries `queryRow` and no aligner runs after it.\n */\nexport const searchEbiPhmmer: SearchBackend = async ({\n  database,\n  ...request\n}) => {\n  const { rows, queryRow, rid } = await queryPhmmer({\n    database: database as PhmmerDatabase,\n    ...request,\n  })\n  return { rid, queryRow, hits: toSearchHits(rows) }\n}\n"],
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+  "names": ["isLaunching", "model", "request", "hasAlignment", "TOOL", "normalizeEbiBlastHits", "result", "hit", "taxid", "ebiBlastResultUrl", "jobId", "queryEbiBlast", "query", "blastDatabase", "maxHits", "onProgress", "onRid", "signal", "hitCount", "snapBlastHitCount", "defaultMaxHits", "job", "runEbiJob", "searchEbiBlast", "database", "request", "TOOL", "phmmerResultUrl", "jobId", "isPhmmerJobId", "buildQueryRow", "rf", "query", "consumed", "row", "c", "parseDescription", "de", "text", "fields", "ox", "sciname", "parseName", "name", "slash", "range", "bare", "parts", "parsePhmmerAlignment", "stockholm", "gc", "gs", "seqdata", "seqname", "StockholmMSA", "id", "description", "parsed", "queryPhmmer", "database", "maxHits", "onProgress", "onRid", "signal", "job", "runEbiJob", "toSearchHits", "rows", "aligned", "rest", "searchEbiPhmmer", "request", "queryRow", "rid"]
+}